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Equal pay protesters stormed into the foyer, chanting, during the announcement of a $1.2 billion hospital for the city, made by English and Health Minister Jonathan Coleman. National MP Michael Woodhouse was also in attendance.
"When they saw us coming in they took off," one protester told the New Zealand Herald. "They went out another door."
Another protester said she saw them cross the road, after chasing them through the building. "They ran away from us," she said.
However a spokeswoman for Dr Coleman said the protesters were overcooking what happened.
She said the ministers were not "chased" but had gone out the back door of the building as planned, to cross the road to the university's graduation parade.
The equal pay march was one of two protests in the city, the other about underfunding in the health system. The health protest was a silent vigil, however.
The drama followed the announcement of the new hospital - the largest build of its type in New Zealand's history.
The new Dunedin Hospital will follow on from the completion of the new $77.8 million Grey Base Hospital on the West Coast, as well as the almost $1 billion hospital redevelopment programme in Canterbury.